The roles of PARP1 in gene control and cell differentiation

Abstract

Cell growth and differentiation during developmental processes require the activation of many inducible genes. However, eukaryotic chromatin, which consists of DNA and histones, becomes a natural barrier impeding access to the functional transcription machinery. To break through the chromatin barrier, eukaryotic organisms have evolved the strategy of using poly(ADP-ribose) polymerase 1 (PARP1) to modulate chromatin structure and initiate the steps leading to gene expression control. As a structural protein in chromatin, enzymatically silent PARP1 inhibits transcription by contributing to the condensation of chromatin, which creates a barrier against gene transcription. However, once activated by environmental stimuli and developmental signals, PARP1 can modify itself and other chromatin-associated proteins, thereby loosening chromatin to facilitate gene transcription. Here we discuss the roles of PARP1 in transcriptional control during development.

Figure 1. Schematic illustration showing PARP1 roles in chromatin gene expression control

(A) The domain structure of the PARP1 protein. The PARP1 protein has the three functional domains: the DNA-binding domain in the N-terminus including three Zn-finger motifs (ZnI, ZnII, ZnIII); Automodification domain (AD) in the central region (374–524) having Glu/Asp and/or lysine residues as indicated for poly(ADP-ribosyl)ation; Catalytic domain in the C-terminus with PARP signature (PS), evolutionarily conserved PARP catalytic site. (B) PARP1 action for transcription control. Hypothetical order of events: 1. RNA polymerase 2 complex initiates transcription. 2. PARP1 is activated, destabilizes chromatin, and automodifies. 3. Automodified PARP1 recruits hnRNP protein from the nucleoplasm, creating high local concentration. 4. PARG proteins cleave pADPr and hnRNPs are released. 5. hnRNP proteins are utilized for hnRNP packaging, stabilization and splicing. Arrow indicates direction of transcription.

Figure 2. Transcription control by PARP1 through chromatin modulation

(A) Transcription inhibition by PARP1 binding to H3 and H4 to compact chromatin. Histone variant, mH2A1, is enriched in the promoter region, which contains such genes as human hsp70, to inhibit PARP1 activity. Chromatin remodeling factor ISWI is also associated with PARP1 in chromatin. (B) Transcription induction by PARP1 activation to destabilize (or “loosen”) chromatin. Activated PARP1 modifies itself, histones (H3, H4) and its variants (mH2A1) and chromatin remodeling factors (ISWI) to destabilize nucleosome structure for transcription induction. (C) Chromatin reassembly by PARG after transcription induction. PARG degrades the pADPr polymer and releases the poly(ADP-ribosy)ated histones and chromatin remodeling factors (ISWI) into the free forms, which will be reassembled into chromatin. Note: histone tetramers is drawn in the nucelosome for simplification instead of histone octamer.

Figure 3. Splicing regulation by poly(ADP-ribosyl)ation of the splicing proteins

(A) Splicing enhancement by poly(ADP-ribosyl)ation of hnRNP A1. HnRNP A1, as the splicing repressor, binds to ISS (intronic splicing silencer) to inhibit the alternative splicing of exon 2 and thereby produce isoform 1. Poly(ADP-ribosyl)ation of hnRNP A1 by PARP1 causes the dissociation of hnRNP A1 from ISS, enhancing the splicing of exon 2 to produce isoform 2. (B) Splicing inhibition by poly(ADP-ribosyl)ation of ASF/SR2. Phosphorylated ASF/SR2 binds to ESE (exonic splicing enhancer) in order to promote the alternative splicing of exon 2 and thereby produce isoform 2. Poly(ADP-ribosyl)ation of ASF/SR2 by PARP1 inhibits phosphorylation of ASF/SR2 and may cause the dissociation of ASF/SR2 from ESE, which inhibits the splicing of exon 2 to produce isoform 1.